Justina Pelletier, the Connecticut teenager who has spent the last year in state custody in a case that has pitted Boston's top doctors against a family who claims their daughter is being medically mistreated, will go into foster care, a court has ruled.

In a two-hour closed door hearing on Monday, Justina's mother "collapsed" and was taken to a local hospital and her father "shouted in anger" when they were told by a Department of Family and Children's judge continued to deny the family custody of their 15-year-old, according to the Boston Globe.

Lou and Linda Pelletier, of West Hartford, Conn., have been fighting for their daughter who they say has mitochondrial disease, a rare genetic disorder with physical symptoms that can affect every part of the body.

Boston Children's Hospital reported the Pelletier's to the Massachusetts Department of Children and Families for suspected child abuse in February 2013. She was confined to its psychiatric unit for treatment for a somatoform disorder for nearly a year before being moved to a residential facility for mental health treatment, according to the family.

"We are just so stressed out," Lou Pelletier, a financial planner and father of three daughters, told ABCNews.com today. "What they put us through yesterday crossed so many lines. My wife has been at the breaking point."

Family court Judge Joseph Johnston has sent Justina to Shared Living Collaborative in Merrimac, a non-medical facility run by the state, according to the family.

The family said they had brought in additional First Amendment lawyers who are opposing a gag order placed on all involved in the case and say they hope to bring Justina home. The custody case has dragged on since last fall and was continued until March 24.

"The court really didn't accomplish much," said Mathew Staves of Liberty Counsel , a conservative organization that advocates for "religious freedom, the sanctity of life, and the family,” who was at hearing.

"She is not doing very well," said Staves. "Linda saw her on Friday … and there were five DCF workers present. There is no private time and she is not allowed to take cell phone photos of her daughter. ... She had red marks on her abdomen and she was very week. It's now the third semester of school since February 2013, and they haven't given her any education, she can't attend church. It's unbelievable."

"If she had somatoform disorder, then her condition would have improved," he said. "She's not gotten any better."

Pelletier had already broken an Essex County family court judge's gag order with ABCNews.com earlier this month, saying, "I have got to save my daughter's life."

Justina was a seemingly healthy teenager performing jumps and spirals at a skating show, then six weeks later, on Feb. 10, 2013, she was in the emergency room at Children's Hospital in Boston after a severe bout with the flu, refusing to eat and barely able to walk, according to her family.

A team of doctors at Boston Children's said her symptoms were psychosomatic, according to the family. The hospital then filed a complaint with the Massachusetts Department of Children and Families, as required by law, because they suspected the parents of child abuse for subjecting their daughter to invasive medical treatments and denying her mental health therapy.

They laid out a treatment plan for Justina, which her parents refused to sign, and on Feb. 14, 2013, when they attempted to check their daughter out of Boston Children's to take her back to Tufts to resume medical treatment, the family said they were told by Boston Children's that they could not discharge Justina.

"We didn't even get a chance to say goodbye," Pelletier said.

Justina was diagnosed with somatoform pain disorder, a psychiatric condition when a person experiences physical pain for which no known medical explanation can be found, according to her family. The case highlights a growing concern among those with rare diseases and autoimmune disorders that physical symptoms that cannot be explained will be dismissed by doctors as psychosomatic.

Lou Pelletier said he and his wife have been only allowed to see their daughter on one-hour weekly supervised visits, first while she was in therapy at Boston Children's psychiatric ward Bader 5, then at a residential treatment center in Framingham, Mass. They say her condition has deteriorated because the hospital has stopped all medical treatment for mitochondrial disease.

The case has enraged advocates for children with mitochondrial disease.

"We feel deeply saddened for Justina and her family today," said Cristy Balcells, executive director of MitoAction. "This is an injustice to the rare disease patient community and to the dedicated and valiant physicians who do the right thing in caring for these patients. Mitochondrial disease is a very complicated illness with complex multi-system problems to treat so we are gravely concerned that Justina's medical needs are not being attended to, and we are concerned that her health will continue to decline without proper medical care."

The Pelletiers reached out to MitoAction for help last year, said Balcells, and they have been speaking on their behalf and providing support.

"We would have expected this to have been wrapped up in December," she told ABCNews.com. "We are truly dismayed that this continues to be prolonged. Justina has lost a year of her life living in an institution without people who care for her – no friends and family, nothing that a typical 15-year-old would have. It's been drawn out because of a political battle and it's not good for the child."

Mitochondrial disease affects the body's ability to make energy, according to Dr. Richard Boles, medical director of Courtagen Life Sciences, a genetic testing company in Massachusetts, and a practicing physician in Los Angeles.

"The symptoms can affect any part of the body," said Boles, who did not treat Justina. "It can cause just about anything. People with mitochondrial disease can have diabetes, autism or other types of retardation, seizure disorders or migraine, chronic fatigue or intestinal failure."

"People with mitochondrial disease have a lot of pain," he told ABCNews.com earlier this month. "Normal sensations are amplified by the nervous system. They are not making it up. The idea of somatoform is you are making it up to serve some need. But they are having real pain."

Dr. Mark Korson, chief of metabolism at Tufts, has been an advocate for Justina, according to the family, who say they worry lack of proper medical care could be fatal for their daughter.

When ABCNews.com called Korson and Tufts Medical Center for comment, they declined, citing patient confidentiality.

Boston Children's Hospital said in a prepared statement to ABCNews.com earlier this month that they "acknowledge the tremendous efforts of our staff in caring for this patient. We are proud of their work and positive impact on the patient."

But the Coalition for Diagnostic Rights, which has also worked closely with the Pelletiers, is critical of the hospital and has called on the DCF to resume medical care for Justina.

"This case could not have developed had it not been for flagrant violations of patients' rights when Justina and her parents arrived at Boston children's Hospital a year ago," said spokeswoman Bridget Mildon. "We continue to demand that these violations be remedied by allowing the parents' original doctor of choice to determine what's in the child's best interests, and to advise the court in that capacity."

Pelletier said he and his wife have been only allowed to see their daughter on one-hour weekly supervised visits. They say her condition has deteriorated because the hospital has stopped all medical treatment for mitochondrial disease.

"She is going off a cliff," Pelletier said of his daughter, who is now confined to a wheelchair. "She looks awful and is pale and her hair is falling out. Her gums are receding and she has no body strength."

"The system has failed," said Justina's father Pelletier. "I am battling the medical world that thinks it knows everything."